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- "Head Case" opens up with Korn's "Twisted Transistor", with Team Gibbs busting the chop shop ring, and then they find a head in the trunk.
- "That's What They Call The Name Of The Game" by either Fort Minor or Styles of Beyond shows DiNozzo getting his ass kicked in basketball during "Light Sleeper".
- R.E.M.'s "Everybody Hurts" in "Grace Period", where Tony visits Jeanne and musters up the courage to tell her he loves her.
- "All We Are" by Matt Nathanson is played at the end of "Family", where Tony comes to terms with the fact that he can't be with Jeanne.
- "Crushcrushcrush" by Paramore is played at the end of "Stakeout", where the team manage to bust the real perpetrator in a sting operation at a bar.
- McGee getting attacked by Butch, who Abby later renames "Jethro", is backed by "Bad Dog, No Biscuit" by Darren Norwood.
- "Judgment Day": Director Shepard tells Tony and Ziva to take the day off from being her bodyguards, DiNozzo rents a car and Tiva drive around Los Angeles as Collective Soul's "Hollywood" adds character to the scenery.
- Performed In-Universe, Cote de Pablo's rendition of "Temptation" by Tom Waits during the season premiere. Fans are treated to fan service from de Pablo as well as her singing chops. A case of The Cast Show Off.
- The conclusion of "Heartland" features a flashback to where Gibbs fondly reminisces about meeting his first wife Shannon. Cue Michael Bublé's "Lost". Heartwarming and tearjerking indeed.
- In the cold open for "Dead Reckoning", a mysterious man engages in a shootout in the sewers against some mooks as Seether's "No Shelter" amplifies the intensity of the action sequence.
- "Legend (Part II)" showcases Kevin Rudolph's "In The City", where Agent Kensi breaks one of her headlights, attracting a band of thugs. They back off when she pulls out her piece.
- At the end of "Outlaws and In-Laws", with Bob Dylan's "California" in the background, Mike Franks and Layla's mother at his house in Mexico, the Mama Bear looks at Mike and she's Not So Stoic after all. Meanwhile, Gibbs tells Vance a story about how two family members who hated each other's guts were in a battle managed to survive by not speaking to one another.
- "Kangaroo Cry" by Blue October plays during the ending montage to the episode "Faith". Between the song and the montage, it is powerful.
- A spine-chilling use of Johnny Cash's "Ain't No Grave" in the penultimate episode of Season 7 that leads to a Cliffhanger.
- "Recruited" ends with Lady Antebellum's "Hello World", where Ducky, with the help of McGee, helps his predecessor Dr. Magnus, played by Bob Newhart, remember all the good he has done; Gibbs successfully vouches for Paul to join the Navy.
- "Pyramid" features "Caught By The Light" by The Boxer Rebellion, during Mike's funeral procession.
- "You Better Watch Out" features "Lounge Christmas" by Emmanuel Fratianni. Tony walks in on his Dad and neighbor in bed, and needs Brain Bleach and to burn the sheets.
- Alternate Roads' "Nothing More" plays at the end of "Homesick," as military families' children affected by a rare disease are cured in time for the holiday season, and as Team Gibbs get ready to celebrate as well.
- The Gumbo Bros. "Keep it Raw" plays in the Cold Open of "Crescent City", the Poorly Disguised Pilot for NCIS: New Orleans, where Dwayne Pride role spends time with his wife, dancing and have a good time.
- During "Honor Thy Father", Warren Zevon's "Keep Me In Your Heart For A While" plays during Jackson Gibbs's funeral, in a touching tribute to the late Ralph Waite.
- Hans Olsen's "Fifty Ups and Fifty Downs" sets a depressed mood for the normally cheerful Elder DiNozzo Senior. Tony finds him wallowing in his apartment after his fiancée left him.
- The entire sequence leading up to Dorneget's Dying Moment of Awesome in Cairo is backed by Imagine Dragon's "Friction".
- "If I Can't Take You with Me" by Heather Stewart at the end of "Personal Day", where Gibbs visits the house in which he once lived with Shannon and Kelly.
- "Say Something" by A Great Big World during "Day In Court". Bishop finds out that Jake has been having an affair at work, and she is heartbroken. This speaks to anyone who's ever been cheated on.
- "Hallelujah" by Leonard Cohen performed by Taye Diggs at the end of "Scope" with the real MusiCorps band. The scenes that follow are Abby watching the performance with Gibbs seemingly on the verge of tears, Tony inviting Ducky, Palmer, and Vance to the expensive Italian restaurant, Bishop and McGee speaking highly of their loved ones with the latter looking up engagement rings online, and Gibbs finally getting over the loss of Shannon and Kelly by choosing to sleep in the bed instead of the couch.
- Tom Odell's "Heal" is played during the final scene of "Reasonable Doubt", where DiNozzo Sr. visits a terminally ill Susan in the hospital. She believes that he is her father, who is actually dead, and from whom she ran away because he couldn't accept that she was gay. Elder DiNozzo poses as her father, apologizing to her for such intolerance. One can't help but think that those were things that could have applied to Junior.DiNozzo Sr.: My wife died, I had to raise a child on my own, I was angry, and I took it out on you. And I had no right to do that.
- The trailer to "Family First", Michael Weatherly's final episode, features Finish Ticket's "Catch You on My Way Out". After thirteen years, it's time to say goodbye to very special agent Anthony DiNozzo. Cue the waterworks.
- At the end of "Being Bad", when Quinn asks Torres about his musical preferences, he dances to "Algo Contigo" by Gente de Zona until Gibbs walks over and turns it off.
- The second-to-last episode of the season, "Something Blue" delivers Timothy McGee and Delilah Fielding's wedding song, "She Blinded Me With Science" by Thomas Dolby.
- "Be Still" by The Fray over the closing montage of Abby's last minutes.
- At the beginning of "Out of the Darkness" the humming of a lullaby can be heard during the recap of the events that led to this episode. Latter on its revealed to be a lullaby that Ziva would sing to her daughter, Tali. It is is played once more during the final moments of the episode as Ziva points a gun at Gibbs, desperate to kill Sahar who is standing behind him and who has been out to kill her, thus keeping Ziva from her family.